8-78656057-G-T

Variant names:

• chr8-78656057-G-T
• rs4739135
• ENST00000661869.2:n.1011+8948C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661869.2(ENSG00000286675):​n.1011+8948C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,038 control chromosomes in the GnomAD database, including 44,916 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.76 (44916 hom., cov: 31)
• Consequence: ENSG00000286675 ENST00000661869.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435
• Publications: 7 publications found

Genes affected

ENSG00000286675 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661869.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286675	ENST00000661869.2		n.1011+8948C>A		intron	N/A
	ENSG00000286675	ENST00000721158.1		n.978+8948C>A		intron	N/A
	ENSG00000286675	ENST00000721159.1		n.978+8948C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116020 AN: 151920 Hom.: 44897 Cov.: 31

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.735

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.764 AC: 116085 AN: 152038 Hom.: 44916 Cov.: 31 AF XY: 0.765 AC XY: 56867 AN XY: 74320

African (AFR) AF: 0.641 AC: 26567 AN: 41456

American (AMR) AF: 0.809 AC: 12351 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2288 AN: 3468

East Asian (EAS) AF: 0.907 AC: 4681 AN: 5160

South Asian (SAS) AF: 0.781 AC: 3766 AN: 4824

European-Finnish (FIN) AF: 0.847 AC: 8975 AN: 10596

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 54957 AN: 67952

Other (OTH) AF: 0.735 AC: 1554 AN: 2114

Alfa AF: 0.767 Hom.: 4786

Bravo AF: 0.757

Asia WGS AF: 0.808 AC: 2808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.26
PhyloP100		0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4739135; hg19: chr8-79568292;